Automatic segmentation

I have passed my MPhil to PhD transfer. Transfers can take a long time: it took me about 2 months to prepare the report and compile results. It is a good idea to write up the transfer report in thesis style keeping in mind that some parts of the transfer report can be recycled to be used in the final thesis.

It is now possible to automatically segment the left atrium using a subdivision and merging algorithm. The atrium is subdivided into disjoint components using some geometric means. These components are then automatically merged using a criterion defined on any two neighboring components. The merging criterion is defined using the notion of a narrowing. Any two neighboring components separated by a narrowing are not allowed to merge. This uses the assumption that the atrium is attached to neighboring structures only through narrow vessels. Allowing the merging to start from the center of the atrium, and stopping the merging at these narrowing can segment the atrium. However, we report that this assumption is not entirely correct. Narrowings can occur within the atrium itself: we have encountered a patient case where the left atrium opens into a pulmonary vein through a narrowing.

Seen above is a surface reconstruction of a left atrium segmented using the automatic scheme described above. A unusual narrowing within the ostium of a pulmonary vein caused the segmentation to miss the pulmonary vein completely. This was corrected by setting a second seed point at the center of the missed vein, and automatically segmenting and merging it with the original segmentation.

Above is my cartoon representation of a left atrium and its surrounding structures. Assume the blue tubular structure to be the ascending aorta, and the green structure to be the pulmonary artery. The left atrium is drawn in red. Using the narrowing scheme we described above, it still becomes difficult to separate the atrium from the pulmonary artery. The artery and the pulmonary veins touch as seen in the figure, and this is due to the partial volume effect. There is no genuine narrowing at these points (where the vein intersects the artery). As a result we have the system thinking that components on either side of this touching point should be merged - causing segmentation to leak into the artery.

We are looking at different ways to overcome this problem. It may be useful to compute the medial axis transform of the vessels. Vessles which touch due to partial volume effects may not have their medial axes touching. We could perhaps exploit this feature and detect where partial volume effect caused non-mergeable components to be merged.

Acknowledgements: The automatic segmentation technique was adopted from John et. al. 2005.